Computational Cancer Biology: An Evolutionary Perspective

ISSN:1553-734XISSN:1553-735

Anytime synthetic projection: Maximizing the probability of goal satisfaction

A projection algorithm is presented for incremental control rule synthesis. The algorithm synthesizes an initial set of goal achieving control rules using a combination of situation probability and estimated remaining work as a search heuristic. This set of control rules has a certain probability of satisfying the given goal. The probability is incrementally increased by synthesizing additional control rules to handle 'error' situations the execution system is likely to encounter when following the initial control rules. By using situation probabilities, the algorithm achieves a computationally effective balance between the limited robustness of triangle tables and the absolute robustness of universal plans

Seeding for pervasively overlapping communities

In some social and biological networks, the majority of nodes belong to multiple communities. It has recently been shown that a number of the algorithms that are designed to detect overlapping communities do not perform well in such highly overlapping settings. Here, we consider one class of these algorithms, those which optimize a local fitness measure, typically by using a greedy heuristic to expand a seed into a community. We perform synthetic benchmarks which indicate that an appropriate seeding strategy becomes increasingly important as the extent of community overlap increases. We find that distinct cliques provide the best seeds. We find further support for this seeding strategy with benchmarks on a Facebook network and the yeast interactome.Comment: 8 Page

A computer algebra user interface manifesto

Many computer algebra systems have more than 1000 built-in functions, making expertise difficult. Using mock dialog boxes, this article describes a proposed interactive general-purpose wizard for organizing optional transformations and allowing easy fine grain control over the form of the result even by amateurs. This wizard integrates ideas including: * flexible subexpression selection; * complete control over the ordering of variables and commutative operands, with well-chosen defaults; * interleaving the choice of successively less main variables with applicable function choices to provide detailed control without incurring a combinatorial number of applicable alternatives at any one level; * quick applicability tests to reduce the listing of inapplicable transformations; * using an organizing principle to order the alternatives in a helpful manner; * labeling quickly-computed alternatives in dialog boxes with a preview of their results, * using ellipsis elisions if necessary or helpful; * allowing the user to retreat from a sequence of choices to explore other branches of the tree of alternatives or to return quickly to branches already visited; * allowing the user to accumulate more than one of the alternative forms; * integrating direct manipulation into the wizard; and * supporting not only the usual input-result pair mode, but also the useful alternative derivational and in situ replacement modes in a unified window.Comment: 38 pages, 12 figures, to be published in Communications in Computer Algebr